Calculate Gene Signature Enrichment Score With Enrichment Test

runSpatialEnrich()

Function to calculate gene signature enrichment scores per spatial position using an enrichment test.

runSpatialEnrich(
    gobject,
    enrich_method = c("PAGE", "rank", "hypergeometric"),
    sign_matrix,
    expression_values = c("normalized", "scaled", "custom"),
    min_overlap_genes = 5,
    reverse_log_scale = TRUE,
    logbase = 2,
    p_value = FALSE,
    n_times = 1000,
    rbp_p = 0.99,
    num_agg = 100,
    max_block = 2e+07,
    top_percentage = 5,
    output_enrichment = c("original", "zscore"),
    name = NULL,
    verbose = TRUE,
    return_gobject = TRUE
)

Arguments

gobject

Giotto object

enrich_method

method for gene signature enrichment calculation

sign_matrix

Matrix of signature genes for each cell type / process

expression_values

expression values to use

min_overlap_genes

minimum number of overlapping genes in sign_matrix required to calculate enrichment (PAGE)

reverse_log_scale

reverse expression values from log scale

logbase

log base to use if reverse_log_scale = TRUE

p_value

calculate p-value (default = FALSE)

n_times

(page/rank) number of permutation iterations to calculate p-value

rbp_p

(rank) fractional binarization threshold (default = 0.99)

num_agg

(rank) number of top genes to aggregate (default = 100)

max_block

number of lines to process together (default = 20e6)

top_percentage

(hyper) percentage of cells that will be considered to have gene expression with matrix binarization

output_enrichment

how to return enrichment output

name

to give to spatial enrichment results, default = PAGE

verbose

be verbose

return_gobject

return Giotto object

Value

A Giotto object or enrichment results if return_gobject = FALSE.

Details

For details see the individual functions: